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Analysis of human SNP data

LINKDATAGEN

A suite of PERL scripts to produce LINKAGE style files from SNP chip data.

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XIBD

An R package to infer X-chromosome identity by descent from SNP data.

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haploclusters

A suite of R scripts to detect excess haplotype sharing in datasets consisting of case and control haplotypes.

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Mutation Age

An R script to estimate mutation age and confidence intervals using the method in Gandolfo, L. C., Bahlo, M., and Speed, T. P. (2014).

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exSTRa

An R package to detect repeat expansions in next-generation sequencing data.

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Bio::SNP::TOPBOT

Perl module and script to find the Illumina TOP/BOT strand of a given SNP, with reference to the forward strand.

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Analysis of gene expression data

brain-coX

An R-shiny application for interactive analysis of microarray gene co-expression datasets from normal human brain tissue. Instructions for usage can be found here.

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BrainGEP

An R package for in-silico gene prioritisation of using the Allen Human Brain Atlas of developing and adult human brain microarray data.

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Analysis of genomic data from microorganisms

moimix

An R package for inferring multiplicity of infection in organisms from high-throughput sequencing data.